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Coexpression cluster:C1125: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!7.45e-78!76;UBERON:0001474!5.43e-71!82;UBERON:0002390!6.19e-71!98;UBERON:0003061!6.19e-71!98;UBERON:0002405!2.48e-70!93;UBERON:0002193!7.08e-65!108;UBERON:0004765!2.96e-63!90;UBERON:0001434!2.58e-55!100;UBERON:0003081!2.32e-27!203;UBERON:0002204!1.13e-26!167;UBERON:0002384!3.04e-14!371;UBERON:0000926!3.01e-12!315;UBERON:0004120!3.01e-12!315;UBERON:0006603!3.01e-12!315
|ontology_enrichment_uberon=UBERON:0002371!7.45e-78!76;UBERON:0001474!5.43e-71!82;UBERON:0002390!6.19e-71!98;UBERON:0003061!6.19e-71!98;UBERON:0002405!2.48e-70!93;UBERON:0002193!7.08e-65!108;UBERON:0004765!2.96e-63!90;UBERON:0001434!2.58e-55!100;UBERON:0003081!2.32e-27!203;UBERON:0002204!1.13e-26!167;UBERON:0002384!3.04e-14!371;UBERON:0000926!3.01e-12!315;UBERON:0004120!3.01e-12!315;UBERON:0006603!3.01e-12!315
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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.100351,1.00019,0.529489,1.62733,1.30874,0.604235,0.226729,0.637583,0.0544999,0.497563,0.647852,0.184039,0.592674,0.905441,0.365029,0.827563,0.786991,0.19568,0.32524,0.384762,0.498384,0.520063,0.897212,0.430372,1.60904,2.1826,0.517892,0.346214,0.150685,1.1974,0.864517,0.714156,1.04347,0.309012,0.442372,0.305874,1.3112,0.282922,0.207499,0.829015,0.459366,1.38248,0.340293,0.265117,0.415364,0.60533,0.486696,0.876276,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,2.66854,0.115253,1.0929,0.179863,0.503161,0.156354,0.782748,0.850825,0.424224,4.08964,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,2.17049,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,1.16062,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,2.27937,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.212606
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1125_anaplastic_CD14_CD14CD16_acute_Macrophage_Dendritic_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:98416663..98416681,-p@chr10:98416663..98416681
-
Hg19::chr10:98416690..98416695,-p@chr10:98416690..98416695
-
Hg19::chr10:98416698..98416709,-p@chr10:98416698..98416709
-
Hg19::chr10:98416729..98416746,-p@chr10:98416729..98416746
-
Hg19::chr1:206945754..206945768,-p5@IL10
Hg19::chr7:112758720..112758727,+p@chr7:112758720..112758727
+
Hg19::chr9:92040335..92040353,-p@chr9:92040335..92040353
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
monopoietic cell8.89e-10559
monocyte8.89e-10559
monoblast8.89e-10559
promonocyte8.89e-10559
macrophage dendritic cell progenitor7.66e-10161
myeloid leukocyte2.76e-9672
defensive cell1.66e-9448
phagocyte1.66e-9448
myeloid lineage restricted progenitor cell4.94e-9266
granulocyte monocyte progenitor cell1.99e-9067
classical monocyte3.26e-8642
CD14-positive, CD16-negative classical monocyte3.26e-8642
myeloid cell5.81e-78108
common myeloid progenitor5.81e-78108
nongranular leukocyte5.15e-58115
leukocyte8.13e-54136
hematopoietic stem cell2.06e-53168
angioblastic mesenchymal cell2.06e-53168
hematopoietic oligopotent progenitor cell2.69e-51161
hematopoietic multipotent progenitor cell2.69e-51161
hematopoietic cell1.08e-49177
hematopoietic lineage restricted progenitor cell5.04e-49120
stuff accumulating cell1.92e-4587
intermediate monocyte4.40e-199
CD14-positive, CD16-positive monocyte4.40e-199
mesenchymal cell3.97e-15354
connective tissue cell1.80e-14361
motile cell3.60e-12386
macrophage1.48e-096
multi fate stem cell2.11e-09427
somatic stem cell5.02e-09433
stem cell1.53e-08441
non-classical monocyte2.76e-083
CD14-low, CD16-positive monocyte2.76e-083
basophil8.20e-073
Uber Anatomy
Ontology termp-valuen
bone marrow7.45e-7876
bone element5.43e-7182
hematopoietic system6.19e-7198
blood island6.19e-7198
immune system2.48e-7093
hemolymphoid system7.08e-65108
skeletal element2.96e-6390
skeletal system2.58e-55100
lateral plate mesoderm2.32e-27203
musculoskeletal system1.13e-26167
connective tissue3.04e-14371
mesoderm3.01e-12315
mesoderm-derived structure3.01e-12315
presumptive mesoderm3.01e-12315


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.